Schema for RepeatMasker - Repeating Elements by RepeatMasker
  Database: mm10    Primary Table: rmsk    Row Count: 5,147,736   Data last updated: 2012-02-06
Format description: RepeatMasker .out record
fieldexampleSQL type description
bin 607smallint(5) unsigned Indexing field to speed chromosome range queries.
swScore 12955int(10) unsigned Smith Waterman alignment score
milliDiv 105int(10) unsigned Base mismatches in parts per thousand
milliDel 9int(10) unsigned Bases deleted in parts per thousand
milliIns 10int(10) unsigned Bases inserted in parts per thousand
genoName chr1varchar(255) Genomic sequence name
genoStart 3000000int(10) unsigned Start in genomic sequence
genoEnd 3002128int(10) unsigned End in genomic sequence
genoLeft -192469843int(11) -#bases after match in genomic sequence
strand -char(1) Relative orientation + or -
repName L1_Mus3varchar(255) Name of repeat
repClass LINEvarchar(255) Class of repeat
repFamily L1varchar(255) Family of repeat
repStart -3055int(11) Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
repEnd 3592int(11) End in repeat sequence
repLeft 1466int(11) -#bases after match (if strand is +) or start (if strand is -) in repeat sequence
id 1char(1) First digit of id field in RepeatMasker .out file. Best ignored.

Sample Rows
 
binswScoremilliDivmilliDelmilliInsgenoNamegenoStartgenoEndgenoLeftstrandrepNamerepClassrepFamilyrepStartrepEndrepLeftid
60712955105910chr130000003002128-192469843-L1_Mus3LINEL1-3055359214661
607121626831105chr130031523003994-192467977-L1Md_FLINEL1-590261712
60723427900chr130039933004054-192467917-L1_Mus3LINEL1-60342972373
60736851992114chr130040403004206-192467765+L1_RodLINEL113211492-43554
60737662310chr130042063004270-192467701+(CAAA)nSimple_repeatSimple_repeat46905
60736851992114chr130042703005001-192466970+L1_RodLINEL114932224-36234
60712802214362chr130050013005439-192466532+L1_RodLINEL124252854-29934
60748532266220chr130054603005548-192466423+Lx9LINEL163096394-12506
607198000chr130055483005570-192466401+(CAAAA)nSimple_repeatSimple_repeat22307
60748532266220chr130055703006764-192465207+Lx9LINEL16395764406

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RepeatMasker (rmsk) Track Description
 

Description

This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked (generally available on the Downloads page). RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below.

Display Conventions and Configuration

In full display mode, this track displays up to ten different classes of repeats:

  • Short interspersed nuclear elements (SINE), which include ALUs
  • Long interspersed nuclear elements (LINE)
  • Long terminal repeat elements (LTR), which include retroposons
  • DNA repeat elements (DNA)
  • Simple repeats (micro-satellites)
  • Low complexity repeats
  • Satellite repeats
  • RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)
  • Other repeats, which includes class RC (Rolling Circle)
  • Unknown

The level of color shading in the graphical display reflects the amount of base mismatch, base deletion, and base insertion associated with a repeat element. The higher the combined number of these, the lighter the shading.

A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that the curator was unsure of the classification. At some point in the future, either the "?" will be removed or the classification will be changed.

Methods

Data are generated using the RepeatMasker -s flag. Additional flags may be used for certain organisms. Repeats are soft-masked. Alignments may extend through repeats, but are not permitted to initiate in them. See the FAQ for more information.

Credits

Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track.

References

Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.

Repbase Update is described in:

Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420. PMID: 10973072

For a discussion of repeats in mammalian genomes, see:

Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):657-63. PMID: 10607616

Smit AF. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev. 1996 Dec;6(6):743-8. PMID: 8994846